RdoA is a bacterial protein kinase from Salmonella enterica serovar Typhimurium first noted for its regulation of dsbA expression in this organism. The crystal structure of RdoA’s homologue, YihE from Escherichia coli, revealed a basic bi-lobal kinase domain that is a hallmark of the eukaryotic Ser/Thr, Tyr protein kinase superfamily. YihE however, bears the greatest structural similarity to choline kinase and aminoglycoside 3’-phosphotransferase [APH(3’)]-IIIa which are both atypical kinases. RdoA and YihE have demonstrated the capacity for autophosphorylation in vitro and the ability to phosphorylate myelin basic protein, however, the native kinase target protein has not been identified. Based on structural alignment with APH(3’)-IIIa, predictions were made of key residues involved in ATP binding and catalysis and five YihE mutants were generated. Both the wildtype and YihE mutants were cloned for expression as N-terminal histidine-tagged proteins. In the work presented here, these proteins have been overexpressed and purified for further study. Mutational analyses revealed that four of the five mutants had decreased kinase activity in comparison to the wildtype protein, thereby establishing the mutated residues as important for enzymatic activity. Several attempts were made to elucidate the substrate of RdoA/YihE, however, it remains unknown. Further investigation is necessary to identify its substrate(s) and to pinpoint its physiological significance. RdoA is a member of the Cpx regulon and its absence stimulates Cpx activation. Since the Cpx system is involved in regulating expression of cell surface appendages and is one of three envelope stress response systems, it is hypothesized that RdoA serves to relay Cpx activation signals. This is supported by studies on the effect of pH on Cpx activity in wildtype and rdoA- cells presented here. RdoA homologues are present in at least 85 different genera. This level of conservation is indicative of an important biological role for this previously uncharacterized bacterial protein kinase. / Thesis (Master, Microbiology & Immunology) -- Queen's University, 2007-12-04 18:19:29.574

With the advantages of low cost, high imaging speed, non-intrusive and non-invasive, electrical capacitance tomography (ECT) becomes one of most maturely developed industrial tomography modalities. However, ECT had not been considered for medical applications before this work. This thesis is to explore medical applications of ECT, especially for root canal treatment (RCT) and revision total hip replacement (THR).A dental ECT system based on impedance analyser has been designed for RCT for two purposes: (1) to visualise the tooth surface in real time and (2) to determine the position of an endodontic file. To adapt the limited space in oral cavity, a miniature two–plate dental ECT sensor with either 2×2 or 2×3 array has been designed and fabricated. The sensor has a similar performance to the conventional ECT sensor and can provide good image quality. By registering and fusing with the radiograph based on a Major-axis method, a real-time image with high resolution can be obtained. A piecewise linear function has been used to locate the axial position of the apex of an endodontic file. The results show that high accuracy can be achieved near the ‘End Point’ as it is one of the reference points, determined by the sudden change in capacitance when a grounded metallic file touches the root apex (conductive media or solution).For revision THR, a conventional 8-electrode single plane sensor has been used, generating real-time 3D images of a metallic rod using a model based method. By this method, the 3D image reconstruction is simplified to estimate the cross-sectional and axial potions of the rod in the sensing area and to draw an image of the rod with prior knowledge. A high accuracy can be achieved with the maximum absolute error of 0.13 cm in estimating cross-sectional position using a weighted mean method and 0.4 cm in estimating axial position by the linear function based on the relative change in capacitance between file and electrodes. A preliminary experiment has been carried out to generate an electrical impedance tomography (EIT) image of a metallic object in conductive solution with high permittivity. Using the impedance analyser based system, the EIT image can be obtained with a conventional ECT sensor and the result is promising, providing the possibility of obtained a real-time EIT 3D image of a milling/drilling tool during revision THR.

Reversible protein phosphorylation is considered the universal language for intracellular communication in all living organisms. This process, catalysed by protein kinases and phosphatases, enables the translation of extracellular signals into cellular responses and also allows for adaptation to a constantly changing environment. In recent years, a number of bacterial eukaryotic-type Ser/Thr protein kinases and phosphatases have been identified. However, their precise functions and substrates are not yet well defined. The genome of opportunistic human pathogen Pseudomonas aeruginosa contains at least five genes encoding putative eukaryotic-type Ser/Thr protein kinases and phosphatases. In the first part of this study, we have attempted to establish the role of Ser/Thr protein kinase PpkA and phosphatase PppA, which belong to type VI secretion system H1-T6SS. Double mutant strain ∆pppA-ppkA was prepared in P. aeruginosa PAO1 background. Phenotypic studies revealed that the mutant grew slower than the wild-type strain in minimal media and exhibited reduced secretion of pigment pyocyanin. In addition, the mutant had altered sensitivity to oxidative and hyperosmotic stress conditions. Consequently, mutant cells had an impaired ability to survive in murine macrophages and an attenuated virulence in the...

La protéine kinase AMPc-dépendante (PKA) joue un rôle crucial dans la régulation neurohormonale de la fonction cardiaque. L’activation aiguë de la PKA est bénéfique car elle conduit à une augmentation de la contraction cardiaque en phosphorylant les acteurs clés du couplage excitation-contraction. En revanche, son activation chronique est délétère et ces effets semblent faire intervenir la régulation de protéines nucléaires pouvant conduire au remodelage hypertrophique et à l'insuffisance cardiaque. La localisation subcellulaire de la PKA, assurée par des protéines d’ancrage (AKAPs), est importante pour la rapidité et la spécificité d’action des hormones mettant en jeu la voie de l’AMPc. Les niveaux d’AMPc sont régulés par l’activité des adénylate cyclases et des phosphodiestérases (PDEs), et l’état de phosphorylation des protéines cibles de la PKA dépend de l’activité des Ser/Thr phosphatases (PPs). Dans le cœur, les PDEs les plus importantes dégradant l’AMPc sont les PDE3 et les PDE4. Les principales PPs cardiaques sont PP1, PP2A et PP2B. Dans une première partie de mon travail, j’ai mis au point, dans les cardiomyocytes de rats adultes, une mesure de l’activité de la PKA en temps réel dans les compartiments cytoplasmiques et nucléaires. J’ai utilisé pour cela des sondes de type AKAR (A-kinase activity reporters) basées sur le transfert d’énergie de fluorescence (FRET) et localisées spécifiquement dans le noyau ou dans le cytoplasme par des séquences d’adressage ou d’exclusion nucléaires. J’ai ainsi pu montrer qu’une stimulation maintenue des récepteurs β-adrénergiques active la PKA de façon plus importante dans le cytoplasme que dans le noyau, et que cette activation se développe lentement au niveau nucléaire que dans le cytoplasme. De ce fait, une stimulation brève des récepteurs β-adrénergiques active maximalement la PKA dans le cytoplasme, mais de façon marginale dans le noyau. Dans une seconde partie de l’étude, je me suis intéressée au rôle des PDE3 et PDE4 ainsi qu’à celui de PP1, PP2A et PP2B dans la régulation de l’activité PKA cytoplasmique et nucléaire, en réponse à une stimulation β-adrénergique. J’ai montré que la PDE4, mais pas la PDE3, régule l’activité de la PKA cytoplasmique et nucléaire. L’utilisation de souris invalidées pour les gènes Pde4b et Pde4d a révélé que l’isoforme PDE4B est prédominante pour la modulation de l’activité PKA cytoplasmique, alors que les deux isoformes PDE4B et PDE4D contribuent à la régulation de l’activité PKA nucléaire. Finalement, j’ai montré que la PP1 et la PP2A, mais pas la PP2B, participent à la terminaison des réponses β-adrénergiques dans le cytoplasme, alors qu’au niveau nucléaire, la PP1 semble jouer un rôle majeur. En conclusion, ce travail a mis en évidence le rôle des phosphodiestérases et des phosphatases dans l’intégration différentielle des réponses PKA à une stimulation β-adrénergique dans le cytoplasme et le noyau de cardiomyocytes adultes. / The cAMP-dependent protein kinase (PKA) exerts short term beneficial effects on cardiac function by phosphorylating several key excitation-contraction coupling (ECC) proteins. However, its chronic activation is deleterious on the long term, and this may involve regulation of nuclear effectors ultimately leading to hypertrophic remodelling and heart failure. The subcellular localization of PKA, mediated by anchoring proteins (AKAPs), is important for the speed and specificity of hormones that activate the cAMP pathway. The levels of cAMP are regulated by adenylyl cyclase and phosphodiesterases (PDEs), and PKA activity is counterbalanced by Ser/Thr phosphatases (PPs). In heart, the most important PDEs that degrade cAMP belong to the PDE3 and PDE4 famillies, whereas the major cardiac PPs are PP1, PP2A and PP2B. In a first part, I developed, in adult rat cardiomyocytes, a technique to measure PKA activity in real time specifically in the cytoplasm and the nucleus. For this I used genetically-encoded fluorescence resonance energy transfer (FRET) sensors called AKAR (A-kinase activity reporters) that can be targeted specifically to the nucleus or the cytoplasm by nuclear localization or exclusion sequences, respectively. Using this approach, I showed that maintained β-adrenergic stimulation activates PKA more efficiently and more potently in the cytoplasm than in the nucleus, and that the kinetics of PKA activation was much slower in the nucleus than in the cytoplasm. Accordingly, a short β-adrenergic stimulation maximally activated PKA in the cytoplasm but marginally activated PKA in the nucleus. In a second part, I characterized the respective contribution of PDE3, PDE4, and PP1, PP2A and PP2B families in the regulation of cytoplasmic and nuclear PKA activity in response to β-adrenergic stimulation. PDE4, but not PDE3, regulates PKA activity in the cytoplasm and in the nucleus. The use of knock out mice for Pde4b and Pde4d genes revealed that PDE4B plays a predominant role to modulate β-AR stimulation of cytoplasmic PKA, whereas in the nucleus both PDE4B and PDE4D isoforms contribute. Finally, I showed that both PP1 and PP2A, but not PP2B, participate to the termination of β-adrenergic PKA responses in the cytoplasm, whereas PP1 appears to play a major role in the nuclei. In conclusion, this work highlights the role of phosphodiesterases and phosphatases in the differential integration of PKA responses to β-adrenergic stimulation in the cytoplasm and the nucleus of adult cardiomyocytes.

The major human pathogen Streptococcus pneumoniae is a unique model for the study of eukaryotic-type serine/threonine protein kinases and its cognate phosphatases in bacteria, since it encodes only a single signaling pair composed of the StkP protein kinase and PhpP phosphatase. This signaling pair plays a role in several cellular processes, mainly in cell wall biosynthesis and cell division. StkP and PhpP proteins with a pleiotropic effect appear to regulate a complex signaling cascade by phosphorylation of many substrates. However, only a few have been characterized so far. Using MS analysis, we have identified about 90 phosphopeptides that are potential substrates for the StkP kinase and PhpP phosphatase. This diploma thesis is focused on the characterization of the new substrate Spr0929 and its role in pneumococcal physiology. One of the objectives was to investigate cell morphology of strains carrying deletion of the spr0929 gene in different genetic backgrounds. It turned out that the role of Spr0929 in cell morphology is strain specific. The growth curves of strains with this deletion were compared to that of the wild type in various physiological conditions as well. As Spr0929 contains a nucleoid-associated domain called NdpA, determination of its cell localization was an important...

Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, is one of the most prevalent infectious diseases in our world today. In order to survive within the host the bacteria need to sense and respond to changes in the environment; however, signal transduction in this bacterium is poorly understood. PknB is a serine/threonine kinase essential for the in vitro survival of M. tuberculosis and therefore a potential drug target against the bacteria. It is the goal of the current study to elucidate downstream substrates of PknB. We have found that PknB shares in vitro substrates with another serine/threonine kinase, PknH, implying the potential complexity of the signaling pathways in the bacteria. We have also provided the first description of the coupling between serine/threonine kinases PknB and PknH with a two-component system response regulator DevR, and further proposed Ser/Thr phosphorylation as the negative regulator of DevR transcription activator activity based on LC-MS/MS analysis. Finally, we have identified a previously unknown phosphoprotein glyceraldehyde 3-phosphate dehydrogenase encoded by the ORF Rv1436, which demonstrates autophosphorylation activity and which phosphorylation is independent of PknB. Overall, the current study has contributed to advance our understanding of the signal transduction pathways and phosphoproteome in Mycobacterium tuberculosis.

Continuous sensation and reaction to environmental fluctuations is especially critical to the survival of unicellular organisms. Stress response mechanisms are essential for cells during the vegetative and sexual life cycles and quiescence. The Schizosaccharomyces pombe mitotic activator and stress response serine/threonine kinase Ssp1 acts independent of the major fission yeast Spc1 MAP kinase stress response cascade. Ssp1 is required at high temperatures in the presence of other stressors, ensures long-term viability in quiescent cells and allows efficient cell division in low-glucose conditions. Ssp1 is cytoplasmic but briefly localizes to the cell membrane after exposure to extracellular stress. It plays a role in actin depolymerization and is required for the change of growth polarity after cell division. After identifying 14-3-3 proteins Rad24 and Rad25 as putative Ssp1 binding partners, we confirmed the interaction with co-immunoprecipitation. Association of Ssp1 with Rad24 diminishes after 15 minutes of hyperosmotic stress, however Rad25 binding is retained. Loss of the rad24 gene product rescues both ssp1- mitotic delay at elevated temperatures and sensitivity to 0. 6M KCl. Conversely, overexpression of rad24 exacerbates ssp1 stress sensitivity and mitotic delay. Diffuse actin polarity and spheroid morphology in rad24- cells improves in an ssp1- background. Ssp1 localization to the cell membrane is negatively regulated by Rad24. Ssp1 does not co-localize with Arp3C (actin-related protein 3 homologue C) after osmotic stress, but instead appears to form a ring around the cell, suggesting localization to fission scars. Ssp1 is basally phosphorylated and hyperphosphorylated after glucose deprivation. Ssp1 is shuttled in and out of the nucleus and accumulates in the nucleus in an exportin Cmr1 dependent manner. Ssp1-GFP levels are constant in all stages of the vegetative cell cycle and Ssp1-GFP is present in both the sexual life cycle and quiescence. C-terminal and N-terminal truncation of ssp1 alters its subcellular localization. The C-terminal region is the site of hyperphosphorylation following glucose deprivation and is also necessary for membrane localization following osmotic stress. / Thesis (Ph.D, Biology) -- Queen's University, 2012-01-24 09:49:58.225

Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, is one of the most prevalent infectious diseases in our world today. In order to survive within the host the bacteria need to sense and respond to changes in the environment; however, signal transduction in this bacterium is poorly understood. PknB is a serine/threonine kinase essential for the in vitro survival of M. tuberculosis and therefore a potential drug target against the bacteria. It is the goal of the current study to elucidate downstream substrates of PknB. We have found that PknB shares in vitro substrates with another serine/threonine kinase, PknH, implying the potential complexity of the signaling pathways in the bacteria. We have also provided the first description of the coupling between serine/threonine kinases PknB and PknH with a two-component system response regulator DevR, and further proposed Ser/Thr phosphorylation as the negative regulator of DevR transcription activator activity based on LC-MS/MS analysis. Finally, we have identified a previously unknown phosphoprotein glyceraldehyde 3-phosphate dehydrogenase encoded by the ORF Rv1436, which demonstrates autophosphorylation activity and which phosphorylation is independent of PknB. Overall, the current study has contributed to advance our understanding of the signal transduction pathways and phosphoproteome in Mycobacterium tuberculosis.

Hip replacement surgery has experienced a dramatic evolution in recent years supported by the latest developments in many areas of technology and surgical procedures. Unfortunately complications that follow hip replacement surgery remains the most challenging dilemma faced both by the patients and medical experts. The thesis presents a novel approach to segment the prosthesis of a THR surgical process by using an Active Contour Model (ACM) that is initiated via an automatically detected seed point within the enarthrosis region of the prosthesis. The circular area is detected via the use of a Fast, Randomized Circle Detection Algorithm. Experimental results are provided to compare the performance of the proposed ACM based approach to popular thresholding based approaches. Further an approach to automatically detect the Obturator Foramen using an ACM approach is also presented. Based on analysis of how medical experts carry out the detection of loosening and subsidence of a prosthesis and the presence of infections around the prosthesis area, this thesis presents novel computational analysis concepts to identify the key feature points of the prosthesis that are required to detect all of the above three types of complications. Initially key points along the prosthesis boundary are determined by measuring the curvature on the surface of the prosthesis. By traversing the edge pixels, starting from one end of the boundary of a detected prosthesis, the curvature values are determined and effectively used to determine key points of the prosthesis surface and their relative positioning. After the key-points are detected, pixel value gradients across the boundary of the prosthesis are determined along the boundary of the prosthesis to determine the presence of subsidence, loosening and infections. Experimental results and analysis are presented to show that the presence of subsidence is determined by the identification of dark pixels around the convex bend closest to the stem area of the prosthesis and away from it. The presence of loosening is determined by the additional presence of dark regions just outside the two straight line edges of the stem area of the prosthesis. The presence of infections is represented by the determination of dark areas around the tip of the stem of the prosthesis. All three complications are thus determined by a single process where the detailed analysis defer. The experimental results presented show the effectiveness of all proposed approaches which are also compared and validated against the ground truth recorded manually with expert user input.

Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, is one of the most prevalent infectious diseases in our world today. In order to survive within the host the bacteria need to sense and respond to changes in the environment; however, signal transduction in this bacterium is poorly understood. PknB is a serine/threonine kinase essential for the in vitro survival of M. tuberculosis and therefore a potential drug target against the bacteria. It is the goal of the current study to elucidate downstream substrates of PknB. We have found that PknB shares in vitro substrates with another serine/threonine kinase, PknH, implying the potential complexity of the signaling pathways in the bacteria. We have also provided the first description of the coupling between serine/threonine kinases PknB and PknH with a two-component system response regulator DevR, and further proposed Ser/Thr phosphorylation as the negative regulator of DevR transcription activator activity based on LC-MS/MS analysis. Finally, we have identified a previously unknown phosphoprotein glyceraldehyde 3-phosphate dehydrogenase encoded by the ORF Rv1436, which demonstrates autophosphorylation activity and which phosphorylation is independent of PknB. Overall, the current study has contributed to advance our understanding of the signal transduction pathways and phosphoproteome in Mycobacterium tuberculosis. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate